Proteins and amino acid-Note

Proteins are complex, organic compounds composed of many amino acids linked together
through peptide bonds and cross-linked between chains by sulfhydryl bonds, hydrogen bonds
and van der Waals forces. There is a greater diversity of chemical composition in proteins than in
any other group of biologically active compounds. The proteins in the various animal and plant
cells confer on these tissues their biological specificity.

Classification

Proteins can be classified as:

(a) Simple proteins. On hydrolysis they yield only the amino acids and occasional small
carbohydrate compounds. Examples are: albumins, globulins, glutelins, albuminoids, histones
and protamines.

(b) Conjugated proteins. These are simple proteins combined with some non-protein material in
the body. Examples are: nucleoproteins, glycoproteins, phosphoproteins, haemoglobins and
lecithoproteins.

(c) Derived proteins. These are proteins derived from simple or conjugated proteins by physical
or chemical means. Examples are: denatured proteins and peptides.

Structure

The potential configuration of protein molecules is so complex that many types of protein
molecules can be constructed and are found in biological materials with different physical
characteristics. Globular proteins are found in blood and tissue fluids in amorphous globular
form with very thin or non-existent membranes. Collagenous proteins are found in connective
tissue such as skin or cell membranes. Fibrous proteins are found in hair, muscle and connective
tissue. Crystalline proteins are exemplified by the lens of the eye and similar tissues. Enzymes
are proteins with specific chemical functions and mediate most of the physiological processes of
life. Several small polypeptides act as hormones in tissue systems controlling different chemical
or physiological processes. Muscle protein is made of several forms of polypeptides that allow
muscular contraction and relaxation for physical movement.

Properties

Proteins can also be characterized by their chemical reactions. Most proteins are soluble in water,
in alcohol, in dilute base or in various concentrations of salt solutions. Proteins have the
characteristic coiled structure which is determined by the sequence of amino acids in the primary
polypeptide chain and the stereo configuration of the radical groups attached to the alpha carbon
of each amino acid. Proteins are heat labile exhibiting various degrees of lability depending upon
type of protein, solution and temperature profile. Proteins can be reversible or irreversible,
denatured by heating, by salt concentration, by freezing, by ultrasonic stress or by aging. Proteins
undergo characteristic bonding with other proteins in the so-called plastein reaction and will
combine with free aldyhyde and hydroxy groups of carbohydrates to form Maillard type
compounds.

 AMINO ACIDS

Essential and Non-essential Amino Acids

Salmon, trout and channel catfish fed diets devoid of arginine, histidine, isoleucine, leucine,
lysine, methionine, phenylalanine, threonine, tryptophan or valine failed to grow (Fig. 3). These
same fish fed diets devoid of other L-amino acids grew as well as fish receiving all 18 amino
acids tested (Fig. 4). The nitrogen component in the test diets was made up of 18 L-amino acids
in the pattern found in whole egg protein. All fish on test recovered rapidly when the missing
amino acid was replaced in the diet. The slope of the growth curve of the recovery group was
identical with that of fish receiving the complete amino acid test diet.

Dispensable amino acids tested were alanine, aspartic acid, cystine, glutamic acid, glycine,
proline, serine, and tyrosine. These amino acids were found to be not essential for the growth of
salmon, trout and channel catfish.

Quantitative studies on the requirements of the 10 indispensable amino acids used a

casein-gelatin mixture supplemented with crystalline L-amino acids. The test diet had an amino
acid pattern of 40 percent whole egg protein for the nitrogen component. Experiments
conducted with carp and eel showed a similar lack of growth when an indispensable amino acid
was absent from the diet.

Function of Proteins
(i) Proteins occur as food reserves as glutelin, globulin casein in milk.  
(ii) Proteins are coagulated in solutions, alkaline to the isoelectric pH by positive ions such
as Zn2+, Cd2+, Hg2+ etc. Casein – pH 4.6, cyt. C – 9.8, resum globulin 5.4, pepsin 2.7,
lysozyme 11.0 etc.
(iii) Proteins are the most diverse molecule on the earth.
(iv) Proteins work as hormone as insulin and glucagon.
(v) Antibiotics as gramicidin, tyrocidin and penicillin are peptides.
(vi) They are structural component of cell.
(vii) They are biological buffers.
(viii) Monellin is the sweetest substance obtained from African berry (2000 time sweeter
than sucrose).
(ix) Proteins helps in defence, movement activity of muscles, visual pigments receptor
molecules, etc.
(x) Natural silk is a polyamide and artificial silk is a polysaccharide. Nitrogen is the basic
constituent.
Functions of Amino Acids
(a) Amino acids are building blocks of proteins and enzymes.
(b) By glycogenolysis, they form glucose.
(c) Hormones like adrenaline and thyroxine are formed with the help of tyrosine.
(d) Antibiotics often contain non-protein amino acids.
(e) They are precursour of many substances.

Structure and Composition

Amino acids are basic units of protein and made up of C, H, O, N and sometimes S. Amino acids
are organic acids with a carboxyl group (–COOH) and one amino group (-NH2) on the a -carbon
atom. Carboxyl group attributes acidic properties and amino group gives basic ones. In solution,
they serve as buffers and help to maintain pH. General formula is R-CHNH2.COOH.
Amino acids are amphoteric or bipolar ions or Zueitter ions. Amino acids link with each other by
peptide bond and long chains are called polypeptide chains.

Classification
Based on R-group of amino acids.
(a) Simple amino acids : These have no functional group in the side chain. e.g. glycine, alanine ,
leucine, valine etc.
(b) Hydroxy amino acids : They have alcohol group in side chain. e.g. threonine, serine, etc.
(c) Sulphur containing amino acids : They have sulphur atom in side chain. e.g. methionine,
cystenine.
(d) Basic amino acids : They have basic group (-NH2) in side chain. e.g. lysine, arginine.
(e) Acidic amino acids : They have carboxyl group in side chain. e.g. aspartic acid, glutamic
acid.
(f) Acid amide amino acids : These are the derivatives of acidic amino acids. In this group, one
of the carboxyl group has been converted to amide (-CONH2). e.g. asparagine, glutamine.
(g) Heterocyclic amino acids : These are the amino acids in which the side chain includes a ring
involving  at least one atom other than carbon. e.g. tryptophan, histidine.
(h) Aromatic amino acids : They have aromatic group (benzene ring) in the side chain. e.g.
phenylalanine, tyrosine, etc.
On the basis of requirements : On the basis of the synthesis amino acids in body and their
requirement, they are categorized as :–
(a) Essential amino acids : These are not synthesized in body hence to be provided in diet e.g.
valine, leucine, isoleucine, theronine ,lysine, etc.
(b) Semi-essential amino acids : Synthesized partially in the body but not at the rate to meet the
requirement of individual. e.g., arginine and histidine.
(c) Non-essential amino acids : These amino acids are derived from carbon skeleton of lipids
and carbohydrate  metabolism. In humans there are 12 non- essential amino acids e.g. alanine,
aspartic acid, cysteine, glutamic acid etc. Proline and hydroxyproline have, NH (imino group)
instead of NH2 hence are called imino acids. Tyrosine can be converted into hormone thyroxine
and adrenaline and skin pigment melanin. Glycine is necessary for production of heme. 
Tryptophan is the precursor of vitamin nicotinamide and auxins. If amino group is removed from
amino acid it can form glucose and if COOH group is removed, it forms amines e.g. histamine.
 Protein folding
Protein folding is the physical process by which a protein chain acquires
its native 3-dimensional structure, a conformation that is usually biologically functional, in an
expeditious and reproducible manner. It is the physical process by which a polypeptide folds into
its characteristic and functional three-dimensional structure from a random coil.

Process of protein folding

Primary structure
The primary structure of a protein, its linear amino-acid sequence, determines its native
conformation. The specific amino acid residues and their position in the polypeptide chain
are the determining factors for which portions of the protein fold closely together and form
its three-dimensional conformation. The amino acid composition is not as important as the
sequence.

Secondary structure

Formation of a secondary structure is the first step in the folding process that a protein takes to
assume its native structure. Characteristic of secondary structure are the structures known
as alpha helices and beta sheets that fold rapidly because they are stabilized
by intramolecular hydrogen bonds, as was first characterized by Linus Pauling. Formation of
intramolecular hydrogen bonds provides another important contribution to protein stability.

Tertiary structure

The alpha helices and beta pleated sheets can be amphipathic in nature, or contain a hydrophilic
portion and a hydrophobic portion. This property of secondary structures aids in the tertiary
structure of a protein in which the folding occurs so that the hydrophilic sides are facing
the aqueous environment surrounding the protein and the hydrophobic sides are facing the
hydrophobic core of the protein.

Quaternary structure
Tertiary structure may give way to the formation of quaternary structure in some proteins, which
usually involves the "assembly" or "coassembly" of subunits that have already folded; in other
words, multiple polypeptide chains could interact to form a fully functional quaternary protein.
Experimental techniques for studying protein folding

● X-ray crystallography
● Fluorescence spectroscopy
● Circular dichroism
● Protein nuclear magnetic resonance spectroscopy
● Biotin painting
● Dual polarisation interferometry
Creatinine
Creatinine is a chemical waste product in the blood that passes through the kidneys to be filtered
and eliminated in urine. The chemical waste is a by-product of normal muscle function. The
more muscle a person has, the more creatinine they produce.

Biological relevance
Serum creatinine (a blood measurement) is an important indicator of kidney health because it is
an easily measured byproduct of muscle metabolism that is excreted unchanged by the kidneys.
Creatinine itself is producedvia a biological system involving creatine, phosphocreatine (also
known as creatine phosphate), and adenosine triphosphate (ATP, the body's immediate energy
supply).
Creatine is synthesized primarily in the liver from the methylation of glycocyamine (guanidino
acetate, synthesized in the kidney from the amino acids arginine and glycine) by S-Adenosyl
methionine. It is then transported through blood to the other organs, muscle, and brain, where,
through phosphorylation, it becomes the high-energy compound phosphocreatine. Creatine
conversion to phosphocreatine is catalyzed by creatine kinase; spontaneous formation of
creatinine occurs during the reaction.
Creatinine is removed from the blood chiefly by the kidneys, primarily by glomerular filtration,
but also by proximal tubular secretion. Little or no tubular reabsorption of creatinine occurs. If
the filtration in the kidney is deficient, blood creatinine concentrations rise. Therefore, creatinine
concentrations in blood and urine may be used to calculate the creatinine clearance (CrCl), which
correlates approximately with the glomerular filtration rate (GFR). Blood creatinine
concentrations may also be used alone to calculate the estimated GFR (eGFR).
The GFR is clinically important because it is a measurement of kidney function. However, in cases of
severe kidney dysfunction, the CrCl rate will overestimate the GFR because hypersecretion of
creatinine by the proximal tubules will account for a larger fraction of the total creatinine
cleared. Ketoacids, cimetidine, and trimethoprim reduce creatinine tubular secretion and,
therefore, increase the accuracy of the GFR estimate, in particular in severe kidney dysfunction.
(In the absence of secretion, creatinine behaves like inulin.)
An alternate estimation of kidney function can be made when interpreting the blood (plasma)
concentration of creatinine along with that of urea. BUN-to-creatinine ratio (the ratio of blood
urea nitrogen to creatinine) can indicate other problems besides those intrinsic to the kidney; for
example, a urea concentration raised out of proportion to the creatinine may indicate a prerenal
problem such as volume depletion.

Antibacterial and potential immunosuppressive properties

Studies indicate creatinine can be effective at killing bacteria of many species in both the Gram
positive and Gram negative as well as diverse antibiotic resistant bacterial strains.Creatinine
appears not to affect growth of fungi and yeast; this can be used to isolate slower growing fungi
free from the normal bacterial populations found in most environmental samples. The
mechanism by which creatinine kills bacteria is not presently known. A recent report also
suggests that creatinine may have immunosuppressive
Serum creatinine
Diagnostic serum creatinine studies are used to determine renal function The reference interval is
0.6-1.3 mg/dL (53-115 µmol/L). Measuring serum creatinine is a simple test, and it is the most
commonly used indicator of renal function.
A rise in blood creatinine concentration is a late marker, observed only with marked damage to
functioning nephrons. Therefore, this test is unsuitable for detecting early-stage kidney disease.
A better estimation of kidney function is given by calculating the estimated glomerular filtration
rate (eGFR). eGFR can be accurately calculated without a 24-hour urine collection using serum
creatinine concentration and some or all of the following variables: sex, age, weight, and race, as
suggested by the American Diabetes Association.  Many laboratories will automatically calculate
eGFR when a creatinine test is requested. Algorithms to estimate GFR from creatinine
concentration and other parameters are discussed in the renal function article.

Urine creatinine
Males produce approximately 150 μmol to 200 μmol of creatinine per kilogram of body weight
per 24 h while females produce approximately 100 μmol/kg/24 h to 150 μmol/kg/24 h. In normal
circumstances, all this daily creatinine production is excreted in the urine.
Creatinine concentration is checked during standard urine drug tests. An expected creatinine
concentration indicates the test sample is undiluted, whereas low amounts of creatinine in the
urine indicate either a manipulated test or low initial baseline creatinine concentrations. Test
samples considered manipulated due to low creatinine are not tested, and the test is sometimes
considered failed.

What are considered high creatinine levels?

● A person with only one kidney may have a normal level of about 1.8 or 1.9.
● Creatinine levels that reach 2.0 or more in babies and 5.0 or more in adults
may indicate severe kidney impairment.
● The need for a dialysis machine to remove wastes from the blood is based
upon several considerations including the BUN, creatinine level, the
potassium level and how much fluid the patient is retaining.
People with only one kidney may have a normal creatinine level of about 1.8 or
1.9. Creatinine levels of 2.0 or more in infants and 5.0 or more in adults may
indicate severe kidney damage. People who are dehydrated may have
elevated creatinine levels.

Albumin
Albumin is a family of globular proteins, the most common of which are
the serum albumins. All the proteins of the albumin family are water-soluble,
moderately soluble in concentrated salt solutions, and experience
heat denaturation. Albumins are commonly found in blood plasma and differ from
other blood proteins in that they are not glycosylated. Substances containing
albumins, such as egg white, are called albuminoids.

Function
Serum albumin is the main protein of human blood plasma. It binds water, cations (such as
Ca2+, Na+ and K+), fatty acids, hormones, bilirubin, thyroxine (T4) and pharmaceuticals
(including barbiturates): its main function is to regulate the oncotic pressure of
blood. Alpha-fetoprotein (alpha-fetoglobulin) is a fetal plasma protein that binds various
cations, fatty acids and bilirubin. Vitamin D-binding protein binds to vitamin D and its
metabolites, as well as to fatty acids. The isoelectric point of albumin is 4.9.
Medical uses
For people with low blood volume, there is no evidence that albumin reduces
mortality when compared with cheaper alternatives such as normal saline, or that
albumin reduces mortality in patients with burns and low albumin levels.
Therefore, the Cochrane Collaboration recommends that it should not be used,
except in clinical trials.
In acoustic droplet vaporization (ADV), albumin is sometimes used as a surfactant.
ADV has been proposed as a cancer treatment by means of occlusion therapy.
Human serum albumin may be used to potentially reverse drug/chemical toxicity
by binding to free drug/agent. Human albumin may also be used in treatment of
decompensated cirrhosis.
Why is albumin important in the blood?
Albumin helps keep fluid in your bloodstream so it doesn't leak into other
tissues. It is also carries various substances throughout your body,
including hormones, vitamins, and enzymes. Low albumin levels can
indicate a problem with your liver or kidneys.
Can low albumin cause hypertension?
Per one SD increment in the albumin concentration the blood pressure
increase was 1-3 mmHg. ... Since albumin, in contrast to high blood
pressure, is considered to be cardioprotective, the two variables
probably affect cardiovascular risk by unrelated mechanisms.

Why is albumin low in heart failure?

Increased excretion (or loss) of albumin from your body from: ...
Certain heart conditions - such as congestive heart failure, or pericarditis -
may cause you to have low albumin levels in your blood. Problems with
your stomach - including inflammatory bowel disease, or lymphoma, can
cause hypoalbuminemia.
amino acid pool
 Denaturation of protein?
Denaturation is a process in which proteins or nucleic acids lose the quaternary
structure, tertiary structure, and secondary structure which is present in their native
state, by application of some external stress or compound such as a
strong acid or base, a concentrated inorganic salt, an organic solvent
(e.g., alcohol or chloroform), radiation or heat.
Denaturants
Protein denaturants
Acids
Acidic protein denaturants include:
● Acetic acid[
● Trichloroacetic acid 12% in water
● Sulfosalicylic acid
Bases
Bases work similarly to acids in denaturation. They include:
● Sodium bicarbonate
Solvents[edit]
Most organic solvents are denaturing, including:
Ethanol
● Alcohol
Cross-linking reagents
Cross-linking agents for proteins include
Formaldehyde
● Glutaraldehyde
Chaotropic agents
Chaotropic agents include:
Urea 6 – 8 mol/l
● Guanidinium chloride 6 mol/l
● Lithium perchlorate 4.5 mol/l
● Sodium dodecyl sulfate
Disulfide bond reducers
Agents that break disulfide bonds by reduction include:
● 2-Mercaptoethanol
● Dithiothreitol
● TCEP (tris(2-carboxyethyl)phosphine)
Other
● Mechanical agitation
● Picric acid
● Radiation
● Temperatur